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- Standardized CPUE of blue shark in the Portuguese pelagic longline fleet operating in the north AtlanticPublication . Coelho, Rui; Santos, Miguel; Lino, PedroThis working document analyzes the catch, effort and standardized CPUE trends for the north Atlantic blue shark captured by the Portuguese pelagic longline fleet. Nominal annual CPUE were calculated as kg/1000 hooks and were standardized with Generalized Linear Models (GLM) and Generalized Linear Mixed Models (GLMM) using year, quarter, area, gear type, targeting effects and area:quarter interactions as fixed factors, and year:area as random effects. Sensitivity analyzes were carried out for the model type (lognormal, tweedie, gamma or delta lognormal), the definition of targeting effects (based on ratios or cluster analysis), and definition of areas. Model goodness-of-fit and comparison was carried out with AIC and the pseudo coefficient of determination (R2 ), and model validation with a residual analysis. The final standardized CPUE trend shows a general increase over the studied period, between 1997 and 2014, with some inter-annual oscillations. This paper presents the first index of abundance for the blue shark estimated from captures from the Portuguese pelagic longline fleet in the North Atlantic, and can be used in future stock assessments models.
- Characterization and standardization of Atlantic sailfish (Istiophorus albicans) catch rates in the east Atlantic from the Portuguese pelagic longline fisheryPublication . Coelho, Rui; Lino, Pedro; Santos, MiguelThis document analyzes the catch, effort and standardized CPUE trends for the eastern Atlantic stock of Atlantic sailfish (Istiophorus albicans) captured by the Portuguese pelagic longline fleet from 1999-2015. Nominal annual CPUE were calculated as kg/1000 hooks and were standardized with Generalized Linear Models (GLM) with Tweedie distribution and using year, quarter, area and targeting effects (ratios) as explanatory variables. Model goodness-of-fit was determined with AIC and the pseudo coefficient of determination, and model validation was analyzed with residual analysis. The final standardized CPUE series shows a general decrease in the initial years, between 1999 and 2010, followed by a general increase in the more recent years, until 2015, with some inter-annual oscillations. This paper presents the first index of abundance for Atlantic sailfish estimated from captures from the Portuguese pelagic longline fleet in the east Atlantic and can be used for future stock assessments of the species
- New observations on the bluefin tuna trap fishery off southern Portugal (NE Atlantic) between 1998-2014: trends on potential catches, catch-at-size and sex ratiosPublication . Santos, Miguel; Rosa, Daniela; Coelho, Rui; Lino, PedroThis paper updates information previously presented on the bluefin tuna catches from a tuna trap fishery operating off the southern coast of Portugal (Algarve). Trends of intra- and interannual catches were analysed and relationships between the potential catches and ICCAT management regulations for the Mediterranean Sea explored. The catch rates of bluefin tuna in the tuna trap off the Algarve remained relatively low between 1998 and 2008, but were followed by increasingly high catches thereafter, with an observed peak during the 2011 season. Significant negative correlations were observed between the catches and the number of allowable fishing months for purse-seines, longlines and bait boats in the Mediterranean Sea, meaning that the catch increased as the number of allowable fishing months for those fishing gears decreased. On the other hand, a positive relationship was observed between the catches and the minimum landing size (MLS), meaning that the catch rates in the tuna trap increased as the MLS for bluefin tuna also increased. These results seem to corroborate other fisheries indicators regarding the recovery of the Eastern Atlantic and Mediterranean Sea stock.
- Modeling species composition and mortality rates of sea turtles in the Portuguese pelagic longline fishery targeting swordfish in the Atlantic Ocean: preliminary results using statistical modelsPublication . Coelho, Rui; Rosa, Daniela; Lino, Pedro; Santos, Miguel
- Observations on small tunas caught in the tuna trap fishery off southern Portugal (NE Atlantic) between 1996 and 2014Publication . Lino, Pedro; Coelho, Rui; Neves dos Santos, MiguelThis study reports on the trends of small tuna catches from a tuna trap operating off the southern coast of Portugal between 1996 and 2014. Landing and catch at size data from one tuna trap were available for bullet tuna (Auxis rochei), Atlantic bonito (Sarda sarda) and little tunny (Euthynnus alletteratus). Trends of intra- and inter-annual catches for the three species were analyzed. Landings occurred mostly during the 2nd and 3rd quarters, with peaks in May for A. rochei and in September for S. sarda and E. alletteratus. Catch at size data shows that similar size ranges of the three species were captured.
- Gelificação dos oceanos – e a culpa não é da alforrecaPublication . Morais, Pedro; Amorim, Katherine; Dias, Ester; Cruz, Joana; Barbosa, Ana; Teodosio, MariaOcean jellification is associated with increasing occurrence of jellyfishes. Jellyfish are gelatinous organisms, with a life cycle composed by sessile stage (polyp) and free living stage (medusa). Blooms jellies, which may have negative impact on fisheries and tourism, are strongly driven by the availability of food, since predators are relatively reduce. The diet of jellies includes small crustacean, egg and fish larvae. Yet, recent UAlg studies showed a much more diverse diet (ex: drifting microbes, terrestrial detritus). Major contributors for ocean jellification are closed connect to men activities and include: (1) excessive input of nutrients (ex: sewage agriculture fertilizers), (2) overfishing of fishes and sea turtles; (3) introduction of artificial structures and (4) changes in hydrological cycle (ex: river dams).
- Membrane and nuclear estrogen receptors in sea bass provide insight to explore genomic and non-genomic estrogenic actions: the mineralized scale examplePublication . Pinto, Patricia IS; Andrade, André; Félix, Rute; Cardoso, João CR; D Estêvão, M; Power, DeborahThe numerous estrogen functions across vertebrates have been classically explained by binding to nuclear estrogen receptors (ERs) regulating the transcription of responsive genes. It is now known that estrogenic compounds can also produce rapid non-genomic actions initiated by binding to plasma estrogen membrane receptors, such as the recently identified G protein-coupled estrogen receptor1 (GPER). Sea bass (Dicentrarchus labrax) express three ER subtype genes, one esr1 and two esr2 genes that appear to have been originated from the original esr2 gene in the teleost-specific whole genome duplication. We have recently identified two genes for GPER in the sea bass genome and phylogenetic analyses also suggest they are teleost-specific gene duplicates. Quantitative PCR revealed a wide tissue distribution for the five receptors in both male and female sea bass and expression throughout the reproductive cycle in brain and pituitary, although with subtype-specific and seasonal differences. When analyzing the sea bass scales, mineralized structures previously shown to be estrogen-responsive, a different receptor repertoire and regulation was detected compared to liver, a classical target gene. In juvenile sea bass scales, the main forms expressed were esr2a and gperb, which were also up regulated after injection with the natural estrogen estradiol (E2) and the phytoestrogen genistein (Gen). Both rapid (30 min) and slow (1 day or more) changes in the activities of enzymes related to mineral turnover were detected in fish scales in response to E2, Gen and xenoestrogens and the gene networks activated 1-5 days after injection of E2 and Gen are being characterized by transcriptomics, revealing both common and compound-specific effects at the transcriptional level. Functional characterization of the three sea bass ER subtypes and two GPERs is underway in mammalian cells, to allow to compare their signaling to different estrogenic compounds. These studies will help to understand the normal estrogen regulation of fish scale functions as well as its possible disruption by phytoestrogens and other xenoestrogens and the relative importance of genomic and non-genomic mechanisms of action of the five receptors.
- A fish scale in vitro bioassay to screen for endocrine disrupting compoundsPublication . Pinto, Patricia IS; Estêvão, Dulce; Santos, Soraia; Andrade, André; Power, DeborahA wide range of natural and anthropogenic compounds are accumulating in the aquatic environment, many of which can interact with and disrupt the endocrine system. Estrogenic endocrine disruptors (EDCs) are a particular problem with impact on humans, ecosystems and wildlife and are particularly relevant in aquatic organisms like fish that may experience life-long exposures. The effects of EDCs in fish have mainly been assessed using reproductive endpoints and in vivo animal experiments. We propose that using other potential endpoints, such as the effect of estrogens on mineralized tissue, would allow development of a simple non invasive assay using scales. Fish scales are mineralized tissues that express both membrane and nuclear estrogen receptors, and are targets for natural estrogens and EDCs. The in vitro bioassay optimized in this work includes sampling of fish scales, incubation in culture media containing the tested compounds and measurement of enzymatic activities related to calcium turnover (TRAP, tartrate-resistant acid phosphatase and ALP, alkaline phosphatase). Several variables were optimized including culture media, compounds concentrations and incubation conditions (e.g. temperature, time), using both sea bass (Dicentrarchus labrax) and tilapia (Oreochromis mossambicus) scales. Significant effects of E2 and EDCs were detected, including both rapid (30 minutes) or slow (1day) changes in scale TRAP or ALP activities, but the responses were of low magnitude and varied with the individual, age, time of year, species and culture conditions. The in vitro fish scale assay is a promising non-invasive screening tool for E2 and EDCs effects, complying with the 3Rs of animal welfare. However, current technical limitations are its limited sensitivity for some parameters eg. TRAP/ALP activity and alternative, sensitive, robust and easy to measure endpoints are under investigation.
- Assessing the effects of Tidal Energy Converter array size on hydrodynamics of Ria Formosa (Portugal)Publication . González-Gorbeña, Eduardo; Pacheco, André; Plomaritis, Theocharis A.; Sequeira, Claudia
- Landscape metrics as indicators of coastal morphology and its use in ecological niche modelling of seagrass speciesPublication . Chefaoui, Rosa M.; Assis, J.; Duarte, Carlos M.; Serrão, EsterDependence of some species on landscape structure has been proved in numerous studies. So far, however, little progress has been made in the integration of landscape metrics in the prediction of species associated with coastal features. Specific landscape metrics were tested as predictors of coastal shape using three coastal features of the Iberian Peninsula (beaches, capes and gulfs) at different scales. We used the landscape metrics in combination with environmental variables to model the niche and find suitable habitats for a seagrass species (Cymodocea nodosa) throughout its entire range of distribution. Landscape metrics able to capture variation in the coastline enhanced significantly the accuracy of the models, despite the limitations caused by the scale of the study. We provided the first global model of the factors that can be shaping the environmental niche and distribution of C. nodosa throughout its range. Sea surface temperature and salinity were the most relevant variables. We identified areas that seem unsuitable for C. nodosa as well as those suitable habitats not occupied by the species. We also present some preliminary results of testing historical biogeographical hypotheses derived from distribution predictions under Last Glacial Maximum conditions and genetic diversity data.